Team:Shanghaitech/HP/Design

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Design of MagicBlock


Why we invented MagicBlock?

Building complex logic genetic circuits is always difficult, especially for common people without biological talents.

We encountered many people during our interview who are enthusiastic about bio-design, yet with little knowledge in synthetic biology and little experience in the lab. Therefore, in order to lower the bar for synthetic circuits and encourage more interdisciplinary people to take part in bio-designs, we came to the idea of using many simple and modularized MagicBlocks to build complex genetic circuits.

The following is the three procedure of using MagicBlock.


What is MagicBlock?


MagicBlock, aiming at testing biological genetic blocks online, is a cloud platform made up of three major parts: a robot, a client software for bio-makers and a data base containing plasmid samples and corresponding sequences. It is freely available and user friendly to the public through their personal computers or other mobile devices.


The following is the three procedure of using MagicBlock.


Fig 1. Three procedures of using Magicblock

1. Search input and output icons using the searching function in our software, build by dragging icons into the page, and upload the design diagram.

2. G code for the uploaded diagram is generated, and is automatically transferred by MagicBlock Cloud Server to the Robot.

3. The Robot transfer the culture media that represent different icons from one to another. The movements of the robot will be live to users.


How can we build parts into blocks?

Genetic circuits are very similar to information processing circuits in IT. Genetic circuits can also be divided into three parts: inputs, signal processing and outputs. In this way, users standardize their ideal genetic circuits using basic circuit icons. Each icon represents a strain of bacteria transformed with plasmids to express a signal processing part.

Take the heavy metal detector as an example, the input signal, heavy metals from environment will be detected by bacteria strain (A) with metal binding proteins and other biological items so that under high metal condition, a signal molecule will be produced.

Thus, through bacteria A (or icon A), heavy metal signals are converted to a signal that can be recognized by another bacteria strain (icon B) based on bacteria quorum sensing system to produce a visible signal such as a green florescence.

Transfer of signals from A to B is achieved by our automated hardware (a robot) which transfers signal containing culture media from A to B to trigger further signal production in B. Therefore, high florescence means high heavy metal condition. As soon as a circuit is confirmed and submitted by users, the robot in real bio-lab will start working. All the movements of the robot as well as experimental results will be live to the users.

Videos

Froffy is a maker from OF COURSE. One day, she came up with this idea: making a bacteria Heat-Triggered Painting Panel.


Fig 2. Froffy's design


Software: How can we build this romantic idea into design diagram using the software?


Guide:

1. come up with a biological application or biodesign;

2. Search parts (inputs/outputs) and decide which logic gates to use.

3. open the client, drag icons from the left column and arrange them with correct order;

4. rename the icons with the parts identity number;

5. link those parts with straight lines. Each line represents a quorum sensing signal transduction;

6. review the diagram, confirm and submit to the platform in the cloud;

7. wait for the robot functioning and free to watch live. Data will be return in time.


Hardware: How is the robot function?


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